Planobacterium oryzisoli sp. nov., a novel bacterium isolated from roots of rice plant

A Gram-negative, aerobic, short rod-shaped, non-motile, non-spore forming bacterium, designated strain GCR5T, was isolated from soil of paddy field. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GCR5T belongs to the genus Planobacterium and is related to Planobacterium taklimakanense NCTC 13490 T (96.1%, 16S rRNA gene sequence similarity). Colonies on R2A were white but they turn into bright yellow after exponential growth. They produce carotenoid pigment after 5-6 days of incubation, before that carotenoid pigment was not found. The major isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C17:0 3OH. Polar lipids include phosphatidylethanolamine, three unidentified phosphoglycolipids, three unidentified glycolipids, one unidentified aminophosphoglycolipid and five unidentified polar lipids. The strain GCR5T was found to have a 2,106,200 bp linear genome with G + C content of 43.7%. The ANI, dDDH and AAI values between the strain GCR5T and the type strains of phylogenetically related species were 60.2-71.1%, 19-24.3%, and 60.2-69.6%, respectively. The strain designated GCR5T produced indole acetic acid (IAA) in the presence of tryptophan only, and auxin responsive genes and tryptophan biosynthesis genes were found in its genome. Based on its polyphasic characteristics, strain GCR5T represents a novel species within the genus Planobacterium, for which the name Planobacterium oryzisoli sp. nov. was proposed. The type strain is GCR5T (= KCTC 82713 T = TISTR 2996 T = TBRC 15746 T).Repositories: The draft genome and 16S rRNA gene sequences of strain GCR5T have been deposited at GenBank/EMBL/DDBJ under accession numbers JADKYY000000000 and MN955408, respectively.

Application of Schizosaccharomyces japonicus in makgeolli fermentation and its brewing characteristics

Recently, unconventional yeasts have become popular as fermentation starters in the brewing industry due to the growing consumer demand for aromatic diversity. Specifically, Schizosaccharomyces japonicus has been explored as a potential starter culture for beer and wine production because of its distinct brewing characteristics; however, its application in makgeolli fermentation has not been tested. Therefore, in the present study, two Sz. japonicus strains (SZJ-1 and SZJ-2) were isolated from natural sources, and their brewing characteristics for makgeolli fermentation were compared with those of commercial S. cerevisiae strain. Although the tested isolates showed a lower fermentation and carbon source consumption rate than control-, their overall alcohol fermentation characteristics were suitable for makgeolli production. Regarding flavor composition, Sz. japonicus-fermented makgeolli possessed more ester compounds (e.g., 2-phenylethyl acetate, ethyl acetate, and ethyl decanoate) than S. cerevisiae-fermented makgeolli. Therefore, Sz. japonicus can be used as an alternative culture starter in makgeolli fermentation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01265-6.

The β-Lactamase Activity at the Community Level Confers β-Lactam Resistance to Bloom-Forming Microcystis aeruginosa Cells

Many freshwater cyanobacteria, including Microcystis aeruginosa, lack several known antibiotic resistance genes; however, both axenic and xenic M. aeruginosa strains exhibited high antibiotic resistance against many antibiotics under our tested concentrations, including colistin, trimethoprim, and kanamycin. Interestingly, axenic PCC7806, although not the xenic NIBR18 and NIBR452 strains, displayed susceptibility to ampicillin and amoxicillin, indicating that the associated bacteria in the phycosphere could confer such antibiotic resistance to xenic strains. Fluorescence and scanning electron microscopic observations revealed their tight association, leading to possible community-level β-lactamase activity. Combinatory treatment of ampicillin with a β-lactamase inhibitor, sulbactam, abolished the ampicillin resistance in the xenic stains. The nitrocefin-based assay confirmed the presence of significant community-level β-lactamase activity. Our tested low ampicillin concentration and high β-lactamase activity could potentially balance the competitive advantage of these dominant species and provide opportunities for the less competitive species, thereby resulting in higher bacterial diversity under ampicillin treatment conditions. Non-PCR-based metagenome data from xenic NIBR18 cultures revealed the dominance of blaOXA-related antibiotic resistance genes followed by other class A β-lactamase genes (AST-1 and FAR-1). Alleviation of ampicillin toxicity could be observed only in axenic PCC7806, which had been cocultured with β-lactamase from other freshwater bacteria. Our study suggested M. aeruginosa develops resistance to old-class β-lactam antibiotics through altruism, where associated bacteria protect axenic M. aeruginosa cells.

Complete genome sequence of Pediococcus acidilactici CACC 537 isolated from canine

Pedi coccus acidilactici CACC 537 was isolated from canine feces and reported to have probiotic properties. We aimed to characterize the potential probiotic properties of this strain by functional genomic analysis. Complete genome sequencing of P. acidilactici CACC 537 was performed using a PacBio RSII and Illumina platform, and contained one circular chromosome (2.0 Mb) with a 42% G + C content. The sequences were annotation revealed 1,897 protein-coding sequences, 15 rRNAs, and 56 tRNAs. It was determined that P. acidilactici CACC 537 genome carries genes known to be involved in the immune system, defense mechanisms, restriction-modification (R-M), and the CRISPR system. CACC 537 was shown to be beneficial in preventing pathogen infection during the fermentation process, help host immunity, and maintain intestinal health. These results provide for a comprehensive understanding of P. acidilactici and the development of industrial probiotic feed additives that can help improve host immunity and intestinal health.

Characterization and Antioxidant Activity of Exopolysaccharides Produced by Lysobacter soyae sp. nov Isolated from the Root of Glycine max L

Microbial exopolysaccharides (EPSs) have attracted attention from several fields due to their high industrial applicability. In the present study, rhizosphere strain CJ11T was isolated from the root of Glycine max L. in Goyang-si, Republic of Korea, and a novel exopolysaccharide was purified from the Lysobacter sp. CJ11T fermentation broth. The exopolysaccharide's average molecular weight was 0.93 × 105 Da. Its monosaccharide composition included 72.2% mannose, 17.2% glucose, 7.8% galactose, and 2.8% arabinose. Fourier-transform infrared spectroscopy identified the exopolysaccharide carbohydrate polymer functional groups, and the structural properties were investigated using nuclear magnetic resonance. In addition, a microstructure of lyophilized EPS was determined by scanning electron microscopy. Using thermogravimetric analysis, the degradation of the exopolysaccharide produced by strain CJ11T was determined to be 210 °C. The exopolysaccharide at a concentration of 4 mg/mL exhibited 2,2-diphenyl-1-picrylhydrazyl free-radical-scavenging activity of 73.47%. Phylogenetic analysis based on the 16S rRNA gene sequencing results revealed that strain CJ11T was a novel isolate for which the name Lysobacter soyae sp. nov is proposed.

Validation of Fuscoporia (Hymenochaetales, Basidiomycota) ITS sequences and five new species based on multi-marker phylogenetic and morphological analyses

Although there is a continuous increase in available molecular data, not all sequence identities in public databases are always properly verified and managed. Here, the sequences available in GenBank for Fuscoporia (Hymenochaetales) were validated. Many morphological characters of Fuscoporia overlap among the species, emphasizing the role of molecular identification for accuracy. The identities of 658 Fuscoporia GenBank internal transcribed spacer (ITS) sequences were assessed using ITS phylogeny, revealing 109 (16.6%) misidentified and 196 (29.8%) unspecified sequences. They were validated and re-identified based on the research articles they were published in and, if unpublished, based on sequences from the type, type locality-derived sequences, or otherwise reliable sequences. To enhance the resolution of species delimitation, a phylogenetic assessment of a multi-marker dataset (ITS + nrLSU + rpb2 + tef1) was conducted. The multi-marker phylogeny resolved five of the twelve species complexes found in the ITS phylogeny and uncovered five new Fuscoporia species: F. dolichoseta, F. gilvoides, F. koreana, F. reticulata, and F. semicephala. The validated ITS sequences in this study may prevent further accumulation of misidentified sequences in public databases and contribute to a more accurate taxonomic evaluation of Fuscoporia species.

Description of Brachybacterium sillae sp. nov., a thermophilic bacterium isolated from a hot spring

The taxonomic position of strain EF45031^T, isolated from the Neungam Carbonate hot spring, was examined using the polyphasic taxonomic approach. Strain EF45031^T shared the highest percentage of 16S rRNA gene sequence with Brachybacterium nesterenkovii CIP 104813 ^T (97.7%). The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between strain EF45031^T and the type strains B. nesterenkovii CIP 104813 ^T and B. phenoliresistens Phenol-A^T were 77.0%, 69.15%, 21.9% and 75.73%, 68.81%, 20.5%, respectively. Phylogenomic analysis using an up-to-date bacterial core gene (UBCG) set revealed that strain EF45031^T belonged to the genus Brachybacterium. Growth occurred between 25 and 50 ℃ at pH 6.0-9.0 and could tolerate salinity up to 5% (w/v). Strain had anteiso-C_15:0 and anteiso-C_17:0 as major fatty acids. Menaquinone-7 (MK-7) was the predominant respiratory menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, three aminolipids, and two unidentified glycolipids. The cell-wall peptidoglycan contained meso-diaminopimelic acid as a diagnostic diamino acid. The genome comprised 2,663,796 bp, with a G + C content of 70.9%. Stress-responsive periplasmic chaperone/protease coding genes were identified in the genome of EF45031^T and were not detected in other Brachybacterium species. The polyphasic taxonomic properties indicate that the strain represents a novel species within the genus Brachybacterium, for which the name Brachybacterium sillae sp. nov. is proposed. The type strain is EF45031^T (= KCTC 49702 ^T = NBRC 115869 ^T).

Identification of the Plant Family Caryophyllaceae in Korea Using DNA Barcoding

Caryophyllaceae is a large angiosperm family, with many species being utilized as ornamental or medicinal plants in Korea, in addition to several endangered species that are managed by the government. In this study, we used DNA barcoding for the accurate identification of Korean Caryophyllaceae. A total of 78 taxa (n = 215) were sequenced based on three chloroplast regions (rbcL, matK, and psbA-trnH) and nuclear ribosomal internal transcribed spacers (ITS). In the neighbor-joining tree, a higher accuracy of identification was generally observed when using ITS (>73%) rather than chloroplast regions (<62%). The highest resolution was found for rbcL + ITS (77.6%), although resolution varied according to the genus. Among the genera that included two and more species, five genera (Eremogone, Minuartia, Pseudostellaria, Sagina, and Stellaria) were successfully identified. However, the species of five other genera (Cerastium, Gypsophila, Dianthus, Silene, and Spergularia) showed relatively low resolutions (0-61.1%). In the cases of Cerastium, Dianthus, and Silene, ambiguous taxonomic relationships among unidentified species may have been a factor contributing to such low resolutions. However, in contrast to these results, Gypsophila and Spergularia have been identified well in previous studies. Our findings indicate the need of taxonomic reconsideration in Korea.

Genetic and demographic signatures accompanying the evolution of the selfing syndrome in Daphne kiusiana, an evergreen shrub

BACKGROUND AND AIMS

The evolution of mating systems from outcrossing to self-fertilization is a common transition in flowering plants. This shift is often associated with the 'selfing syndrome', which is characterized by less visible flowers with functional changes to control outcrossing. In most cases, the evolutionary history and demographic dynamics underlying the evolution of the selfing syndrome remain poorly understood.

METHODS

Here, we characterize differences in the demographic genetic consequences and associated floral-specific traits between two distinct geographical groups of a wild shrub, Daphne kiusiana, endemic to East Asia; plants in the eastern region (southeastern Korea and Kyushu, Japan) exhibit smaller and fewer flowers compared to those of plants in the western region (southwestern Korea). Genetic analyses were conducted using nuclear microsatellites and chloroplast DNA (multiplexed phylogenetic marker sequencing) datasets.

KEY RESULTS

A high selfing rate with significantly increased homozygosity characterized the eastern lineage, associated with lower levels of visibility and herkogamy in the floral traits. The two lineages harboured independent phylogeographical histories. In contrast to the western lineage, the eastern lineage showed a gradual reduction in the effective population size with no signs of a severe bottleneck despite its extreme range contraction during the last glacial period.

CONCLUSIONS

Our results suggest that the selfing-associated morphological changes in D. kiusiana are of relatively old origin (at least 100 000 years ago) and were driven by directional selection for efficient self-pollination. We provide evidence that the evolution of the selfing syndrome in D. kiusiana is not strongly associated with a severe population bottleneck.

Qualitative and Quantitative Analysis of the Major Bioactive Components of Juniperus chinensis L. Using LC-QTOF-MS and LC-MSMS and Investigation of Antibacterial Activity against Pathogenic Bacteria

Plants in the genus Juniperus have been reported to produce a variety of chemical components, such as coumarins, flavonoids, lignans, sterols, and terpenoids. Here, ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) and ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) were applied to qualitatively and quantitatively analyze the major bioactive components in an ethanolic crude extract from the leaves of Juniperus chinensis L., which grows naturally in Korea. In addition, the antibacterial activity of the crude extract against pathogenic bacteria was investigated. Using LC-QTOF-MS analysis, we identified ten compounds, of which six were confirmed to be flavonoid and lignan-based components as the major bioactive components, i.e., isoquercetin, quercetin-3-O-α-l-rhamnoside, hinokiflavone, amentoflavone, podocarpusflavone A, and matairesinoside. Among them, a quantitative analysis performed using LC-MS/MS revealed that the levels of quercetin-3-O-α-l-rhamnoside and amentoflavone in the crude extract were 203.78 and 69.84 mg/g, respectively. Furthermore, the crude extract exhibited potential antibacterial activity against 10 pathogenic bacteria, with the highest antibacterial activity detected against Bordetella pertussis. Thus, further studies of the leaf extract of J. chinensis L. must be carried out to correlate the compounds present in the extract with the antibacterial activity and elucidate the mechanisms of action of this extract against bacteria.

Rheinheimera faecalis sp. nov., isolated from Ceratotherium simum feces

A novel strain YR1^T, Gram-stain-negative, rod-shaped, catalase- and oxidase-positive, and aerobic bacterium, was isolated from the feces of Ceratotherium simum. The strain grew at 9-42 °C (optimal temperature, 30 °C), at pH 6.0-10.0 (optimal pH, 7.0), and in the presence of 0-3% (w/v) NaCl (optimal salinity, 0%). Phylogenetic analyses based on 16S rRNA gene sequencing indicated that strain YR1^T was most closely related to Rheinheimera soli BD-d46^T (98.6%), R. riviphila KYPC3^T (98.6%), and R. mangrovi LHK 132^T (98.1%). Moreover, the average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain YR1^T and R. mangrovi LHK 132 ^T were 88.3%, 92.1%, and 35.3%, respectively, indicating that strain YR1^T is a novel species in the genus Rheinheimera. The genome size and genomic DNA G + C content of strain YR1^T were 4.5 Mbp and 46.37%, respectively. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol, while the predominant respiratory quinone was Q-8. Summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), C_{16: 0}, and summed feature 8 (C_18:1 ω7c) were the primary cellular fatty acids (> 16%). Based on these genotypic and phenotypic characteristics, strain YR1^T was identified as a novel species in the genus Rheinheimera, for which the name Rheinheimera faecalis sp. nov. is proposed, with the type strain is YR1^T (= KACC 22402^T = JCM 34823^T).

Slit-Robo expression in the leech nervous system: insights into eyespot evolution

BACKGROUND

Slit and Robo are evolutionarily conserved ligand and receptor proteins, respectively, but the number of slit and robo gene paralogs varies across recent bilaterian genomes. Previous studies indicate that this ligand-receptor complex is involved in axon guidance. Given the lack of data regarding Slit/Robo in the Lophotrochozoa compared to Ecdysozoa and Deuterostomia, the present study aims to identify and characterize the expression of Slit/Robo orthologs in leech development.

RESULTS

We identified one slit (Hau-slit), and two robo genes (Hau-robo1 and Hau-robo2), and characterized their expression spatiotemporally during the development of the glossiphoniid leech Helobdella austinensis. Throughout segmentation and organogenesis, Hau-slit and Hau-robo1 are broadly expressed in complex and roughly complementary patterns in the ventral and dorsal midline, nerve ganglia, foregut, visceral mesoderm and/or endoderm of the crop, rectum and reproductive organs. Before yolk exhaustion, Hau-robo1 is also expressed where the pigmented eye spots will later develop, and Hau-slit is expressed in the area between these future eye spots. In contrast, Hau-robo2 expression is extremely limited, appearing first in the developing pigmented eye spots, and later in the three additional pairs of cryptic eye spots in head region that never develop pigment. Comparing the expression of robo orthologs between H. austinensis and another glossiphoniid leech, Alboglossiphonia lata allows to that robo1 and robo2 operate combinatorially to differentially specify pigmented and cryptic eyespots within the glossiphoniid leeches.

CONCLUSIONS

Our results support a conserved role in neurogenesis, midline formation and eye spot development for Slit/Robo in the Lophotrochozoa, and provide relevant data for evo-devo studies related to nervous system evolution.

Possible species discrimination of a blotched nerite Nerita albicilla with their distribution pattern and demographic history in the Indo-Pacific

The blotched nerite Nerita albicilla (Linnaeus 1758) is distributed in intertidal areas of the Indo-Pacific. In South Korea, it has been found only in the southernmost region of Jeju Island so far. Owing to its limited distribution, it can be a promising intertidal species helpful for monitoring global climate change effects in the Korean Peninsula. We performed population genetic analyses based on 393 COI haplotypes from 697 N. albicilla, including 167 from this study and 530 from public databases. The results showed that there are two distinct genetic lineages in N. albicilla: PAIO (Palearctic, Australasia, Indo-Malay, and Oceania) and Afrotropic lineages. DNA barcoding gap analyses indicated that the two lineages could be differentiated into two different species: N. albicilla (PAIO) and N. originalis sp. nov. (Afrotropic) (3.96%). Additionally, it was revealed that their divergence time was ca. 5.96 Ma and dramatic diversification of COI haplotypes occurred during the late Pliocene and Pleistocene. The results of MDA, BSP, and neutrality test implied recent population size expansion, which was estimated to be ca. 250 Ka. Finally, we discussed whether the observation of N. originalis sp. nov. in South Korea is due to the northward migration through ocean currents caused by global warming or due to artificial activity through marine transportation.

Resistant starch utilization by Bifidobacterium, the beneficial human gut bacteria

Resistant starch (RS) reaches the large intestine largely intact, where it is fermented by the gut microbiota, resulting in the production of short-chain fatty acids (SCFAs) that have beneficial effects on the human body. Bifidobacteria are a major species widely used in the probiotic field, and are increased in the gut by RS, indicating their importance in RS metabolism in the intestine. Bifidobacteria have a genetic advantage in starch metabolism as they possess a significant number of starch-degrading enzymes and extraordinary three RS-degrading enzymes, allowing them to utilize RS. However, to date, only three species of RS-degrading bifidobacteria have been reported as single isolates B. adolescentis, B. choerinum, and B. pseudolongum. In this review, we describe recent studies on RS utilization by Bifidobacterium, based on their biochemical characteristics and genetic findings. This review provides a crucial understanding of how bifidobacteria survive in specific niches with abundant RS such as the human gut.

Description of Defluviimonas salinarum sp. nov. with the potential of benzene-degradation isolated from saltern in the Yellow Seacoast

Strain CAU 1641T was isolated from saltern collected in Ganghwa Island, Republic of Korea. The bacterium was an aerobic, Gram-negative, catalase-positive, oxidase-positive, motile, and rod-shaped bacterium. Cell of strain CAU 1641T could grow at 20-40°C and pH 6.0-9.0 with 1.0-3.0% (w/v) NaCl. Stain CAU 1641T shared high 16S rRNA gene sequence similarities with Defluviimonas aquaemixtae KCTC 42108T (98.0%), Defluviimonas denitrificans DSM 18921T (97.6%), and Defluviimonas aestuarii KACC 16442T (97.5%). Phylogenetic trees based on the 16S rRNA gene and the core-genome sequences indicated that strain CAU 1641T belonged to genus Defluviimonas. Strain CAU 1641T contained ubiquinone-10 (Q-10) as the sole respiratory quinone and and summed feature 8 (C18:1ω6c and/or C18:1ω7c) as the predominant fatty acid (86.1%). The pan-genome analysis indicated that the genomes of the strain CAU 1641T and 15 reference strains contain a small core genome. The Average Nucleotide Identity and digital DNA-DNA hybridization values among strain CAU 1641T and reference strains of the genus Defluviimonas were in the range of 77.6%-78.8% and 21.1-22.1%, respectively. The genome of strain CAU 1641T has several genes of benzene degradation. The genomic G + C content was 66.6%. Based on polyphasic and genomic analyses, strain CAU 1641T represents a novel species of the genus Defluviimonas, for which the name Defluviimonas salinarum sp. nov., is proposed. The type strain is CAU 1641T ( = KCTC 92081T = MCCC 1K07180T).

Anti-inflammatory effects of Athyrium yokoscense extract via inhibition of the Erk1/2 and NF-κB pathways in bisphenol A-stimulated A549 cells

Bisphenol A is an environmental endocrine disruptor that has similar functions to estrogen in humans. However, few studies have investigated pulmonary inflammation induced by BPA, and the effect of Athyrium yokoscense extract on this inflammatory response is unknown. In this study, we investigated this effect in A549 human alveolar epithelial cells. BPA at concentrations higher than 100 µM were cytotoxic to A549 cells at 24 and 48 h after treatment; however, AYE (100 µg/mL) had a protective effect against BPA-induced cytotoxicity. AYE also inhibited the generation of intracellular reactive oxygen species, expressions of cyclooxygenase-2 and extracellular signal-regulated kinase1/2 proteins, activities of phospholipase A2, COX-2, nuclear factor kappa-light-chain-enhancer of activated B cells, and proinflammatory mediators including prostaglandin E2, tumor necrosis factor-α, and interleukin-6 induced by BPA in A549 cells. This study demonstrated that BPA, which induces chronic lung disease, causes oxidative stress and inflammatory response in lung epithelial cell line, and found that AYE reduces BPA-induced oxidative stress and inflammatory response by down-regulating the Erk1/2 and NF-κB pathways.

Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato)

A multifunctional, Gram-stain-negative, aerobic, motile by flagella, short-rod shaped bacteria, designated strain RG36^T was isolated from roots of marigold plant (Tagetes patula) sampled at Dongguk University, Republic of Korea. A 16S rRNA sequences indicated that the closest phylogenetic neighbors were Paraburkholderia acidiphila 7Q-K02^T (99.0%) and Paraburkholderia sacchari IPT101^T (98.9%) of the family Burkholderiaceae. The draft genome size was 8.52 Mb (63.7% GC). The genome contained 7,381 coding sequences. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strain RG36^T with its most closely related species were only 83.1-88.7 and 27.6-36.7%, respectively. Strain RG36^T contained Q-8 as the major respiratory quinone and its main fatty acids (>10%) were C_16:0, C_17:0 cyclo, C_19:0 cyclo ω8c, and summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c). Strain RG36^T accumulates polyhydroxybutyrates (PHB) and exhibits multiple plant growth-promoting properties including production of indole-3-acetic acid (IAA), siderophores, protease, phosphate solubilization, and harboring gene clusters for its multifunctional properties. A pot experiment was conducted to evaluate the effect of PGPR on the growth of Solanum lycopersicum L. (Tomato). Result also confirmed the ability of strain RG36^T to promote tomato plant growth, especially it increases the yield of tomatoes. Structural assessment of the bioplastic by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and GC-MS spectroscopy, which confirmed the structure of the polymer as PHB. Our study revealed the potential of strain RG36^T to promote the growth of tomato plant and fruit yield by stimulating the various phytohormones, which could be use as bio-fertilizers to reduce the use of chemical fertilizers and promotes sustainable agricultural production. The phenotypic, chemotaxonomic and phylogenetic data, and genome analysis showed that strain RG36^T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia tagetis sp. nov. is proposed. The type strain is RG36^T (=KACC 22685^T = TBRC 15696^T).

Germ Cell Isolation and Cryopreservation from Reproductive Organs of Brown Mealworm

This study aimed to isolate and freeze germ cells from the superior brown mealworm. Styrofoam diet changes were observed for 20 days to determine whether mealworms were useful insects for decomposing Styrofoam. The average weight of mealworms before the Styrofoam diet was 500 mg, which decreased to 336 mg at D20 after their diet. To preserve mealworms with excellent Styrofoam-degrading ability, we first isolated the reproductive organs of mealworms, testes, ovaries, sperms, and ovarioles. Morphologically, male and female adult brown mealworms were distinguished according to the presence or absence of a protrusion at the tip of the fifth segment of the abdomen. Sperms and ovarioles were observed in anatomically isolated testes and ovaries. We compared mechanical and enzymatic (collagenase I) methods to effectively isolate ovarioles from adult female brown mealworms. For the enzymatic method, most were torn and burst as the membrane of the ovarioles was damaged by collagenase I, unlike the mechanical method. To preserve the superior genetic resources of mealworms, we cryopreserved the ovaries of female brown mealworms using slow-freezing and vitrification. Histological analysis showed that the yolk sac was completely damaged in the ovaries after slow-freezing. However, only partial damage was achieved in the vitrification group compared to the control group (no freezing). The newly developed vitrification method with alginate-encapsulated ovarioles maintained the yolk sac in the ovarioles but was evenly distributed. These results provide basic data for reproductive studies of other useful insects and contribute to the biobanking and fertility preservation of superior mealworm germ cells and endangered insects.

Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles

A wide range of environmental factors heavily impact aquatic ecosystems, in turn, affecting human health. Toxic organic compounds resulting from anthropogenic activity are a source of pollution in aquatic ecosystems. To evaluate these contaminants, current approaches mainly rely on acute and chronic toxicity tests, but cannot provide explicit insights into the causes of toxicity. As an alternative, genome-wide gene expression systems allow the identification of contaminants causing toxicity by monitoring the organisms' response to toxic substances. In this study, we selected 22 toxic organic compounds, classified as pesticides, herbicides, or industrial chemicals, that induce environmental problems in aquatic ecosystems and affect human-health. To identify toxic organic compounds using gene expression data from Daphnia magna, we evaluated the performance of three machine learning based feature-ranking algorithms (Learning Vector Quantization, Random Forest, and Support Vector Machines with a Linear kernel), and nine classifiers (Linear Discriminant Analysis, Classification And Regression Trees, K-nearest neighbors, Support Vector Machines with a Linear kernel, Random Forest, Boosted C5.0, Gradient Boosting Machine, eXtreme Gradient Boosting with tree, and eXtreme Gradient Boosting with DART booster). Our analysis revealed that a combination of feature selection based on feature-ranking and a random forest classification algorithm had the best model performance, with an accuracy of 95.7%. This is a preliminary study to establish a model for the monitoring of aquatic toxic substances by machine learning. This model could be an effective tool to manage contaminants and toxic organic compounds in aquatic systems.

Host habitat is the major determinant of the gut microbiome of fish

BACKGROUND

Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish.

RESULTS

We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals).

CONCLUSIONS

Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.

Molecular Phylogeny and Taxonomy of the Genus Spumella (Chrysophyceae) Based on Morphological and Molecular Evidence

The genus Spumella, established by Cienkowsky in 1870, is characterized by omnivory, two (rarely three) flagella, a short stick-like structure beneath the flagella, a threadlike stalk, cell division via constriction and cyst formation. Since the first phylogenetic study of Spumella-like flagellates, their paraphyly has consistently been shown, with separation into several genera. More recently, Spumella was carefully investigated using molecular and morphological data to propose seven new species. Classification of this genus and knowledge of its species diversity remain limited because Spumella-like flagellates are extremely difficult to identify based on limited morphological characters. To understand the phylogeny and taxonomy of Spumella, we analyzed molecular and morphological data from 47 strains, including 18 strains isolated from Korean ponds or swamps. Nuclear SSU, ITS and LSU rDNA data were used for maximum likelihood and Bayesian analyses. The molecular data divided the strains into 15 clades, including seven new lineages, each with unique molecular signatures for nuclear SSU rRNA from the E23-2 to E23-5 domains, the spacer between the E23-8 and E23-9 domains of the V4 region and domain 29 of the V5 region. Our results revealed increased species diversity in Spumella. In contrast to the molecular phylogeny results, the taxa showed very similar cell morphologies, suggesting morphological convergence into simple nanoflagellates to enable heterotrophy. Three new species produced stomatocysts in culture. Aspects of stomatocyst morphology, including collar structure, surface ornamentation, and cyst shape, were very useful in differentiating the three species. The general ultrastructure of Spumella bureschii strain Baekdongje012018B8 and S. benthica strain Hwarim032418A5 showed the typical chrysophyte form for the leucoplast, a vestigial chloroplast surrounded by four envelope membranes, supporting the hypothesis that Spumella evolved from a phototroph to a heterotroph via the loss of its photosynthetic ability. Seven new species are proposed: S. benthica, S. communis, S. longicolla, S. oblata, S. rotundata, S. similis, and S. sinechrysos.

Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae)

Iris is one of the largest genera in the family Iridaceae, comprising hundreds of species, including numerous economically important horticultural plants used in landscape gardening and herbal medicine. Improved taxonomic classification of Iris species, particularly the endangered Korean-native Iris, is needed for correct species delineation. To this end, identification of diverse genetic markers from Iris genomes would facilitate molecular identification and resolve ambiguous classifications from molecular analyses; however, only two Iris plastid genomes, from Iris gatesii and Iris sanguinea, have been sequenced. Here, we used high-throughput next-generation sequencing, combined with Sanger sequencing, to construct the plastid genomes of 14 Korean-native Iris species with one outgroup and predict their gene content. Using these data, combined with previously published plastid genomes from Iris and one outgroup (Sisyrinchium angustifolium), we constructed a Bayesian phylogenetic tree showing clear speciation among the samples. We further identified sub-genomic regions that have undergone neutral evolution and accurately recapitulate Bayesian-inferred speciation. These contain key markers that could be used to identify and classify Iris samples into taxonomic clades. Our results confirm previously reported speciation patterns and resolve questionable relationships within the Iris genus. These data also provide a valuable resource for studying genetic diversity and refining phylogenetic relationships between Iris species.

An integrative approach to the systematics of the Berthella californica species complex (Heterobranchia: Pleurobranchidae)

Berthella californica (W. H. Dall, 1900) is a widespread species of heterobranch sea slug distributed across the North Pacific Ocean, from Korea and Japan to the Galapagos Islands. Two distinct morphotypes are observed in B. californica, which differ in external coloration, egg-mass morphology and geographic distribution (with the exception of a small range overlap in Southern California). Molecular and morphological data obtained in this study reveals that these two morphotypes constitute distinct species. The name B. californica (type locality: San Pedro, California) is retained for the southern morphotype, whereas the name Berthella chacei (J. Q. Burch, 1944) (type locality: Crescent City, California) is resurrected for the northern morphotype. Moreover, molecular phylogenetic analyses recovered B. californica as sister to Berthellina, in a well-supported clade separate from Berthella, suggesting that the classification of B. californica may need additional revision.

Yellow sea mediated segregation between North East Asian Dryophytes species

While comparatively few amphibian species have been described on the North East Asian mainland in the last decades, several species have been the subject of taxonomical debates in relation to the Yellow sea. Here, we sampled Dryophytes sp. treefrogs from the Republic of Korea, the Democratic People's Republic of Korea and the People's Republic of China to clarify the status of this clade around the Yellow sea and determine the impact of sea level change on treefrogs' phylogenetic relationships. Based on genetics, call properties, adult morphology, tadpole morphology and niche modelling, we determined the segregated status species of D. suweonensis and D. immaculatus. We then proceeded to describe a new treefrog species, D. flaviventris sp. nov., from the central lowlands of the Republic of Korea. The new species is geographically segregated from D. suweonensis by the Chilgap mountain range and known to occur only in the area of Buyeo, Nonsan and Iksan in the Republic of Korea. While the Yellow sea is the principal element to the current isolation of the three clades, the paleorivers of the Yellow sea basin are likely to have been the major factor for the divergences within this clade. We recommend conducting rapid conservation assessments as these species are present on very narrow and declining ranges.

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

BACKGROUND

Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge.

RESULTS

To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858-151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power.

CONCLUSIONS

The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as super-barcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.